Hervé Rey

Modelling and simulation of the architecture and development of the oil-palm (Elaeis guineensis Jacq.) root system. I. The model

The objective of this work was to model the architecture and growth dynamics of the oil-palm root system. The morphological and functional unit of the root system, called “root architectural unit” and its development sequence enabled us to establish the basis of a mathematical formalization of the root system architecture. The topology of the branched structures and the processes of growth, branching and mortality were described and modelled by stochastic processes (graph model, automata, laws of probability). The models obtained were then combined with geometrical parameters in an overall mathematical model: the reference axis. Simulation of this model provided 3-D numerical models. Validations of the overall model based on comparing the 3-D numerical models with observed root systems, appeared satisfactory.

Modelling and simulation of the architecture and development of the oil-palm (#Elaeis guineensis# Jacq.) root system : II. Estimation of root parameters using the RACINES postprocessor

A stochastic model of oil-palm (Elaeis guineensis Jacq.) root system architecture and development has been developed. This model enabled us to create 3-D numerical models of complete root systems by simulation. The application of a postprocessor software, called “RACINES”, to these 3-D numerical models, provided an estimation of some parameters of plant root systems. The objective of this paper is to present oil-palm root characteristics as possible outputs of the application of this RACINES software. The outputs described in this article cover (i) spatial distribution of roots under plantation conditions, (ii) the estimation and distribution of total root biomass, per root type or per soil horizon and (iii) the location and quantification of absorbent surfaces. The computing techniques used were based on voxellization of space and creation of 3-D virtual sceneries exactly reproducing observed planting designs. By comparing the results of observations and simulations for spatial distribution (by trench wall density maps) and root biomasses (by real and virtual sampling) we were able to carry out additional numerical validations of the model.

Integrated responses of rosette organogenesis, morphogenesis and architecture to reduced incident light in Arabidopsis thaliana results in higher efficiency of light interception

Plants have a high phenotypic plasticity in response to light. We investigated changes in plant architecture in response to decreased incident light levels in Arabidopsis thaliana (L.) Heynh, focusing on organogenesis and morphogenesis, and on consequences for the efficiency of light interception of the rosette. A. thaliana ecotype Columbia plants were grown under various levels of incident photosynthetically active radiation (PAR), with blue light (BL) intensity proportional to incident PAR intensity and with a high and stable red to far-red light ratio. We estimated the PAR absorbed by the plant, using data from precise characterisation of the light environment and 3-dimensional simulations of virtual plants generated with AMAPsim software. Decreases in incident PAR modified rosette architecture; leaf area decreased, leaf blades tended to be more circular and petioles were longer and thinner. However, the efficiency of light interception by the rosette was slightly higher in plants subjected to lower PAR intensities, despite the reduction in leaf area. Decreased incident PAR delayed leaf initiation and slowed down relative leaf expansion rate, but increased the duration of leaf expansion. The leaf initiation rate and the relative expansion rate during the first third of leaf development were related to the amount of PAR absorbed. The duration of leaf expansion was related to PAR intensity. The relationships identified could be used to analyse the phenotypic plasticity of various genotypes of Arabidopsis. Overall, decreases in incident PAR result in an increase in the efficiency of light interception.

Using a 3-D virtual sunflower to simulate light capture at organ, plant and plot levels : Contribution of organ interception, impact of heliotropism and analysis of genotypic differences

BACKGROUND AND AIMS Light interception is a critical factor in the production of biomass. The study presented here describes a method used to take account of architectural changes over time in sunflower and to estimate absorbed light at the organ level. METHODS The amount of photosynthetically active radiation absorbed by a plant is estimated on a daily or hourly basis through precise characterization of the light environment and three-dimensional virtual plants built using AMAP software. Several treatments are performed over four experiments and on two genotypes to test the model, quantify the contribution of different organs to light interception and evaluate the impact of heliotropism. KEY RESULTS This approach is used to simulate the amount of light absorbed at organ and plant scales from crop emergence to maturity. Blades and capitula were the major contributors to light interception, whereas that by petioles and stem was negligible. Light regimen simulations showed that heliotropism decreased the cumulated light intercepted at the plant scale by close to 2.2% over one day. CONCLUSIONS The approach is useful in characterizing the light environment of organs and the whole plant, especially for studies on heterogeneous canopies or for quantifying genotypic or environmental impacts on plant architecture, where conventional approaches are ineffective. This model paves the way to analyses of genotype-environment interactions and could help establish new selection criteria based on architectural improvement, enhancing plant light interception.

Architectural analysis and modelling of the branching process of the young oil-palm root system.

An architectural analysis of the root system of young oil-palm (Elaeis guineensis Jacq.) seedlings was made. In this analysis, root branching was modelled by a Markov chain (discrete-time, discrete-state space stochastic process). This study has been realized on radicles of young oil-palm seedlings which were considered as main axes which branch. We defined an elementary length unit as the smallest length between two successive lateral roots. The model was based on the analysis of a sequence of events, each event being indexed by the rank of the elementary length unit on the main axis. An event was defined as the state of the length unit, chosen between unbranched state and three branched-state categories. The branching process of the oil-palm radicle was modelled by a four-state first-order Markov chain. Consequently, the state of an elementary length unit depended only on the state of the previous one. The Markov chain was homogeneous, i.e. the transition probabilities did not depend on the rank of the elementary length unit.This study allowed us to identify a probabilistic model of root branching which was the first step in the elaboration of a stochastic model of the architecture of the oil-palm root system.

Which processes drive fine root elongation in a natural mountain forest ecosystem

Background: Quantifying the dynamics of root growth is vital when characterising the role of vegetation in carbon cycling. Aims: We examined the temporal dynamics of root growth and responses to spatial (altitude, forest patchiness and soil depth) and biological factors (root diameter and root topology) in mid-montane and upper montane coniferous forest ecosystems. Methods: Using rhizotrons, two indicators were investigated: occurrence, i.e. the proportion of roots which had elongated since the previous measurement of root elongation (%), and daily root elongation speed (mm d−1) once the elongation occurred. Results: Spatial factors had a limited effect on root growth. Roots in the same diameter class possessed different elongation speeds and this was related to topological ranking, reflecting a disparity in physiological activity. Temporally, the occurrence of root elongation reached a peak in May–October (up to 90%) and sharply dropped after October 2010. The maximum root elongation speed (mean: 3.0 mm d−1) was measured in July–August. Root growth was the most inactive in February 2011 but some roots still exhibited positive elongation speeds (mean: 0.5 mm d−1). Occurrence and speed of elongation reacted differently with regard to environmental and biological factors. Conclusions: Temporal and biological factors contributed more towards explaining the variability of root growth than spatial factors. In future studies, both occurrence and speed of elongation should be used to characterise root growth.

Estimation of light interception in research environments: a joint approach using directional light sensors and 3D virtual plants applied to sunflower (Helianthus annuus) and Arabidopsis thaliana in natural and artificial conditions

Light interception is a major factor influencing plant development and biomass production. Several methods have been proposed to determine this variable, but its calculation remains difficult in artificial environments with heterogeneous light. We propose a method that uses 3D virtual plant modelling and directional light characterisation to estimate light interception in highly heterogeneous light environments such as growth chambers and glasshouses. Intercepted light was estimated by coupling an architectural model and a light model for different genotypes of the rosette species Arabidopsis thaliana (L.) Heynh and a sunflower crop. The model was applied to plants of contrasting architectures, cultivated in isolation or in canopy, in natural or artificial environments, and under contrasting light conditions. The model gave satisfactory results when compared with observed data and enabled calculation of light interception in situations where direct measurements or classical methods were inefficient, such as young crops, isolated plants or artificial conditions. Furthermore, the model revealed that A. thaliana increased its light interception efficiency when shaded. To conclude, the method can be used to calculate intercepted light at organ, plant and plot levels, in natural and artificial environments, and should be useful in the investigation of genotype-environment interactions for plant architecture and light interception efficiency.

A minimal continuous model for simulating growth and development of plant root systems

Aims: This paper proposes a general and minimal continuous model of root growth that aggregates architectural and developmental information and that can be used at different spatial scales. Methods: The model is described by advection, diffusion and reaction operators, which are related to growth processes such as primary growth, branching, mortality and root death. Output variable is the number of root tips per unit volume of soil. Operator splitting techniques are used to fit, solve and analyze the model with regards to ontogeny. The modeling approach is illustrated on a 2D case study concerning a part of Eucalyptus root system. Results: Operator splitting is helpful to fit the model. Basic knowledge on root architecture and development allows decreasing the number of unknown parameters and defining ontogenic phases on which specific calibrations must be carried out. Simulation results reproduce quantitatively the dynamic evolution of root density distribution with a good accuracy. Conclusion: The proposed root growth model is based on a continuous formalism that can be easily coupled with other physical models, e.g. nutrient and water transfer. The equations are generic and allow simulating different root architectures and growth strategies. They can be efficiently solved using adapted numerical methods.

Characterizing above- and belowground carbon partitioning in forest trees along an altitudinal gradient using area-based indicators

Abstract Characterizing the above- and belowground carbon stocks of ecosystems is vital for a better understanding of the role of vegetation in carbon cycling. Yet studies on forest ecosystems at high altitudes remain scarce. We examined above- and belowground carbon partitioning in trees growing in mixed montane/upper montane forest ecosystems in the French Alps. Field work was performed in three forests along a gradient of both altitude (1400 m, 1700 m, and 2000 m) and altitude-induced species composition (from lower altitude Abies alba and Fagus sylvatica to higher altitude Picea abies and Pinus uncinata). We performed forest inventories and root sampling along soil wall profiles, so that the stand basal area (SBA, in m2 ha-1) and root cross-sectional area (RCSA, in m2 ha-1) were estimated at each altitude. To characterize the carbon allocation trend between the above-and belowground compartments, the ratio of RCSA to SBA was then calculated. We found that both SBA and RCSA of coarse roots (diameter > 2 mm) were significantly different among the three altitudes. No significant difference in RCSA of fine roots (diameter ≤ 2 mm) was found among altitudes. The ratio of RCSA of fine roots to SBA augmented with increasing elevation, suggesting that forest ecosystems at higher altitudes allocate more carbon from above- to belowground organs. This increased allocation to fine roots would allow trees to scavenge nutrients more efficiently throughout the short growing season. Furthermore, this work highlighted the interest of using easy to measure area-based indicators as proxies of root and stem biomass when investigating carbon partitioning in highly heterogeneous montane/upper montane forests.

Architectural analysis of root system of sexually vs. vegetatively propagated yam (Dioscorea rotundata Poir.), a tuber monocot

Architectural descriptors were used to understand root system structure and development in white yam (Dioscorea rotundata Poir., Dioscoreaceae), a tuber monocot. Observations were made on seedlings and plant derived from tuber fragments, cultivated in greenhouses over a developmental cycle. This study demonstrated that both seedlings and plants derived from tubers have two distinct root systems that are highly organized. The first (seminal or tubercular) has been called the temporary root system which is small and short lived. The architectural unit here is made up of two root axis categories. The second (adventitious in both cases) has been called the definitive root system. It is larger and has a far longer lifespan than temporary root systems. The architectural unit here is made up of three root axis categories. Adventitious root systems are formed by structural repetitions of their own architectural unit. The temporary and definitive root systems possess the same structural and functional properties and become established and succeed one another in time following an identical developmental sequence. Neo tuber development is coupled with the root system development. Our results highlight to what extent it is important to study simultaneously the different parts of a root system in order to understand its development. This study confirms how architectural tools can be used to understand root system structure and development and prove accurate informations on root system development for use in agricultural management.